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4. Single cell dynamics of tumor specificity vs bystander activity in CD8+ T cells define the diverse immune landscapes in colorectal cancer

Author

Borràs, Daniel Morales, Verbandt, Sara, Ausserhofer, Markus, Sturm, Gregor, Lim, Jinyeong, Verge, Gil Arasa, Vanmeerbeek, Isaure, Laureano, Raquel S., Govaerts, Jannes, Sprooten, Jenny, Hong, Yourae, Wall, Rebecca, De Hertogh, Gert, Sagaert, Xavier, Bislenghi, Gabriele, D’Hoore, André, Wolthuis, Albert, Finotello, Francesca, Park, Woong-Yang, Naulaerts, Stefan, Tejpar, Sabine, and Garg, Abhishek D.

Published
2023
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5. CD4+ T cell activation distinguishes response to anti-PD-L1+anti-CTLA4 therapy from anti-PD-L1 monotherapy

Author

Franken, Amelie, Bila, Michel, Mechels, Aurelie, Kint, Sam, Van Dessel, Jeroen, Pomella, Valentina, Vanuytven, Sebastiaan, Philips, Gino, Bricard, Orian, Xiong, Jieyi, Boeckx, Bram, Hatse, Sigrid, Van Brussel, Thomas, Schepers, Rogier, Van Aerde, Cedric, Geurs, Sarah, Vandecaveye, Vincent, Hauben, Esther, Vander Poorten, Vincent, Verbandt, Sara, Vandereyken, Katy, Qian, Junbin, Tejpar, Sabine, Voet, Thierry, Clement, Paul M., and Lambrechts, Diether

Published
2024
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7. Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer

Author

Joanito, Ignasius, Wirapati, Pratyaksha, Zhao, Nancy, Nawaz, Zahid, Yeo, Grace, Lee, Fiona, Eng, Christine L. P., Macalinao, Dominique Camat, Kahraman, Merve, Srinivasan, Harini, Lakshmanan, Vairavan, Verbandt, Sara, Tsantoulis, Petros, Gunn, Nicole, Venkatesh, Prasanna Nori, Poh, Zhong Wee, Nahar, Rahul, Oh, Hsueh Ling Janice, Loo, Jia Min, Chia, Shumei, Cheow, Lih Feng, Cheruba, Elsie, Wong, Michael Thomas, Kua, Lindsay, Chua, Clarinda, Nguyen, Andy, Golovan, Justin, Gan, Anna, Lim, Wan-Jun, Guo, Yu Amanda, Yap, Choon Kong, Tay, Brenda, Hong, Yourae, Chong, Dawn Qingqing, Chok, Aik-Yong, Park, Woong-Yang, Han, Shuting, Chang, Mei Huan, Seow-En, Isaac, Fu, Cherylin, Mathew, Ronnie, Toh, Ee-Lin, Hong, Lewis Z., Skanderup, Anders Jacobsen, DasGupta, Ramanuj, Ong, Chin-Ann Johnny, Lim, Kiat Hon, Tan, Emile K. W., Koo, Si-Lin, Leow, Wei Qiang, Tejpar, Sabine, Prabhakar, Shyam, and Tan, Iain Beehuat

Published
2022
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9. Image-based multiplex immune profiling of cancer tissues: translational implications. A report of the International Immuno-oncology Biomarker Working Group on Breast Cancer

Author

Pathologie, Cancer, Jahangir, Chowdhury Arif, Page, David B., Broeckx, Glenn, Gonzalez, Claudia A., Burke, Caoimbhe, Murphy, Clodagh, Reis-Filho, Jorge S., Ly, Amy, Harms, Paul W., Gupta, Rajarsi R., Vieth, Michael, Hida, Akira I., Kahila, Mohamed, Kos, Zuzana, van Diest, Paul J., Verbandt, Sara, Thagaard, Jeppe, Khiroya, Reena, Abduljabbar, Khalid, Acosta Haab, Gabriela, Acs, Balazs, Adams, Sylvia, Almeida, Jonas S., Alvarado-Cabrero, Isabel, Azmoudeh-Ardalan, Farid, Badve, Sunil, Baharun, Nurkhairul Bariyah, Bellolio, Enrique R., Bheemaraju, Vydehi, Blenman, Kim R.M., Botinelly Mendonça Fujimoto, Luciana, Burgues, Octavio, Chardas, Alexandros, Cheang, Maggie Chon U., Ciompi, Francesco, Cooper, Lee A.D., Coosemans, An, Corredor, Germán, Dantas Portela, Flavio Luis, Deman, Frederik, Demaria, Sandra, Dudgeon, Sarah N., Elghazawy, Mahmoud, Fernandez-Martín, Claudio, Fineberg, Susan, Fox, Stephen B., Giltnane, Jennifer M., Gnjatic, Sacha, Gonzalez-Ericsson, Paula I., Grigoriadis, Anita, Halama, Niels, Hanna, Matthew G., Harbhajanka, Aparna, Hart, Steven N., Hartman, Johan, Hewitt, Stephen, Horlings, Hugo M., Husain, Zaheed, Irshad, Sheeba, Janssen, Emiel A.M., Kataoka, Tatsuki R., Kawaguchi, Kosuke, Khramtsov, Andrey I., Kiraz, Umay, Kirtani, Pawan, Kodach, Liudmila L., Korski, Konstanty, Akturk, Guray, Scott, Ely, Kovács, Anikó, Lænkholm, Anne Vibeke, Lang-Schwarz, Corinna, Larsimont, Denis, Lennerz, Jochen K., Lerousseau, Marvin, Li, Xiaoxian, Madabhushi, Anant, Maley, Sai K., Manur Narasimhamurthy, Vidya, Marks, Douglas K., McDonald, Elizabeth S., Mehrotra, Ravi, Michiels, Stefan, Kharidehal, Durga, Minhas, Fayyaz ul Amir Afsar, Mittal, Shachi, Moore, David A., Mushtaq, Shamim, Nighat, Hussain, Papathomas, Thomas, Penault-Llorca, Frederique, Perera, Rashindrie D., Pinard, Christopher J., Pinto-Cardenas, Juan Carlos, Pruneri, Giancarlo, Pusztai, Lajos, Rajpoot, Nasir Mahmood, Rapoport, Bernardo Leon, Rau, Tilman T., Ribeiro, Joana M., Rimm, David, Vincent-Salomon, Anne, Saltz, Joel, Sayed, Shahin, Hytopoulos, Evangelos, Mahon, Sarah, Siziopikou, Kalliopi P., Sotiriou, Christos, Stenzinger, Albrecht, Sughayer, Maher A., Sur, Daniel, Symmans, Fraser, Tanaka, Sunao, Taxter, Timothy, Tejpar, Sabine, Teuwen, Jonas, Thompson, E. Aubrey, Tramm, Trine, Tran, William T., van der Laak, Jeroen, Verghese, Gregory E., Viale, Giuseppe, Wahab, Noorul, Walter, Thomas, Waumans, Yannick, Wen, Hannah Y., Yang, Wentao, Yuan, Yinyin, Bartlett, John, Loibl, Sibylle, Denkert, Carsten, Savas, Peter, Loi, Sherene, Specht Stovgaard, Elisabeth, Salgado, Roberto, Gallagher, William M., Rahman, Arman, Pathologie, Cancer, Jahangir, Chowdhury Arif, Page, David B., Broeckx, Glenn, Gonzalez, Claudia A., Burke, Caoimbhe, Murphy, Clodagh, Reis-Filho, Jorge S., Ly, Amy, Harms, Paul W., Gupta, Rajarsi R., Vieth, Michael, Hida, Akira I., Kahila, Mohamed, Kos, Zuzana, van Diest, Paul J., Verbandt, Sara, Thagaard, Jeppe, Khiroya, Reena, Abduljabbar, Khalid, Acosta Haab, Gabriela, Acs, Balazs, Adams, Sylvia, Almeida, Jonas S., Alvarado-Cabrero, Isabel, Azmoudeh-Ardalan, Farid, Badve, Sunil, Baharun, Nurkhairul Bariyah, Bellolio, Enrique R., Bheemaraju, Vydehi, Blenman, Kim R.M., Botinelly Mendonça Fujimoto, Luciana, Burgues, Octavio, Chardas, Alexandros, Cheang, Maggie Chon U., Ciompi, Francesco, Cooper, Lee A.D., Coosemans, An, Corredor, Germán, Dantas Portela, Flavio Luis, Deman, Frederik, Demaria, Sandra, Dudgeon, Sarah N., Elghazawy, Mahmoud, Fernandez-Martín, Claudio, Fineberg, Susan, Fox, Stephen B., Giltnane, Jennifer M., Gnjatic, Sacha, Gonzalez-Ericsson, Paula I., Grigoriadis, Anita, Halama, Niels, Hanna, Matthew G., Harbhajanka, Aparna, Hart, Steven N., Hartman, Johan, Hewitt, Stephen, Horlings, Hugo M., Husain, Zaheed, Irshad, Sheeba, Janssen, Emiel A.M., Kataoka, Tatsuki R., Kawaguchi, Kosuke, Khramtsov, Andrey I., Kiraz, Umay, Kirtani, Pawan, Kodach, Liudmila L., Korski, Konstanty, Akturk, Guray, Scott, Ely, Kovács, Anikó, Lænkholm, Anne Vibeke, Lang-Schwarz, Corinna, Larsimont, Denis, Lennerz, Jochen K., Lerousseau, Marvin, Li, Xiaoxian, Madabhushi, Anant, Maley, Sai K., Manur Narasimhamurthy, Vidya, Marks, Douglas K., McDonald, Elizabeth S., Mehrotra, Ravi, Michiels, Stefan, Kharidehal, Durga, Minhas, Fayyaz ul Amir Afsar, Mittal, Shachi, Moore, David A., Mushtaq, Shamim, Nighat, Hussain, Papathomas, Thomas, Penault-Llorca, Frederique, Perera, Rashindrie D., Pinard, Christopher J., Pinto-Cardenas, Juan Carlos, Pruneri, Giancarlo, Pusztai, Lajos, Rajpoot, Nasir Mahmood, Rapoport, Bernardo Leon, Rau, Tilman T., Ribeiro, Joana M., Rimm, David, Vincent-Salomon, Anne, Saltz, Joel, Sayed, Shahin, Hytopoulos, Evangelos, Mahon, Sarah, Siziopikou, Kalliopi P., Sotiriou, Christos, Stenzinger, Albrecht, Sughayer, Maher A., Sur, Daniel, Symmans, Fraser, Tanaka, Sunao, Taxter, Timothy, Tejpar, Sabine, Teuwen, Jonas, Thompson, E. Aubrey, Tramm, Trine, Tran, William T., van der Laak, Jeroen, Verghese, Gregory E., Viale, Giuseppe, Wahab, Noorul, Walter, Thomas, Waumans, Yannick, Wen, Hannah Y., Yang, Wentao, Yuan, Yinyin, Bartlett, John, Loibl, Sibylle, Denkert, Carsten, Savas, Peter, Loi, Sherene, Specht Stovgaard, Elisabeth, Salgado, Roberto, Gallagher, William M., and Rahman, Arman

Published
2024

10. Image-based multiplex immune profiling of cancer tissues:translational implications. A report of the International Immuno-oncology Biomarker Working Group on Breast Cancer

Author

Jahangir, Chowdhury Arif, Page, David B., Broeckx, Glenn, Gonzalez, Claudia A., Burke, Caoimbhe, Murphy, Clodagh, Reis-Filho, Jorge S., Ly, Amy, Harms, Paul W., Gupta, Rajarsi R., Vieth, Michael, Hida, Akira I., Kahila, Mohamed, Kos, Zuzana, van Diest, Paul J., Verbandt, Sara, Thagaard, Jeppe, Khiroya, Reena, Abduljabbar, Khalid, Acosta Haab, Gabriela, Acs, Balazs, Adams, Sylvia, Almeida, Jonas S., Alvarado-Cabrero, Isabel, Azmoudeh-Ardalan, Farid, Badve, Sunil, Baharun, Nurkhairul Bariyah, Bellolio, Enrique R., Bheemaraju, Vydehi, Blenman, Kim R.M., Botinelly Mendonça Fujimoto, Luciana, Burgues, Octavio, Chardas, Alexandros, Cheang, Maggie Chon U., Ciompi, Francesco, Cooper, Lee A.D., Coosemans, An, Corredor, Germán, Dantas Portela, Flavio Luis, Deman, Frederik, Demaria, Sandra, Dudgeon, Sarah N., Elghazawy, Mahmoud, Fernandez-Martín, Claudio, Fineberg, Susan, Fox, Stephen B., Giltnane, Jennifer M., Gnjatic, Sacha, Gonzalez-Ericsson, Paula I., Grigoriadis, Anita, Halama, Niels, Hanna, Matthew G., Harbhajanka, Aparna, Hart, Steven N., Hartman, Johan, Hewitt, Stephen, Horlings, Hugo M., Husain, Zaheed, Irshad, Sheeba, Janssen, Emiel A.M., Kataoka, Tatsuki R., Kawaguchi, Kosuke, Khramtsov, Andrey I., Kiraz, Umay, Kirtani, Pawan, Kodach, Liudmila L., Korski, Konstanty, Akturk, Guray, Scott, Ely, Kovács, Anikó, Lænkholm, Anne Vibeke, Lang-Schwarz, Corinna, Larsimont, Denis, Lennerz, Jochen K., Lerousseau, Marvin, Li, Xiaoxian, Madabhushi, Anant, Maley, Sai K., Manur Narasimhamurthy, Vidya, Marks, Douglas K., McDonald, Elizabeth S., Mehrotra, Ravi, Michiels, Stefan, Kharidehal, Durga, Minhas, Fayyaz ul Amir Afsar, Mittal, Shachi, Moore, David A., Mushtaq, Shamim, Nighat, Hussain, Papathomas, Thomas, Penault-Llorca, Frederique, Perera, Rashindrie D., Pinard, Christopher J., Pinto-Cardenas, Juan Carlos, Pruneri, Giancarlo, Pusztai, Lajos, Rajpoot, Nasir Mahmood, Rapoport, Bernardo Leon, Rau, Tilman T., Ribeiro, Joana M., Rimm, David, Vincent-Salomon, Anne, Saltz, Joel, Sayed, Shahin, Hytopoulos, Evangelos, Mahon, Sarah, Siziopikou, Kalliopi P., Sotiriou, Christos, Stenzinger, Albrecht, Sughayer, Maher A., Sur, Daniel, Symmans, Fraser, Tanaka, Sunao, Taxter, Timothy, Tejpar, Sabine, Teuwen, Jonas, Thompson, E. Aubrey, Tramm, Trine, Tran, William T., van der Laak, Jeroen, Verghese, Gregory E., Viale, Giuseppe, Wahab, Noorul, Walter, Thomas, Waumans, Yannick, Wen, Hannah Y., Yang, Wentao, Yuan, Yinyin, Bartlett, John, Loibl, Sibylle, Denkert, Carsten, Savas, Peter, Loi, Sherene, Specht Stovgaard, Elisabeth, Salgado, Roberto, Gallagher, William M., Rahman, Arman, Jahangir, Chowdhury Arif, Page, David B., Broeckx, Glenn, Gonzalez, Claudia A., Burke, Caoimbhe, Murphy, Clodagh, Reis-Filho, Jorge S., Ly, Amy, Harms, Paul W., Gupta, Rajarsi R., Vieth, Michael, Hida, Akira I., Kahila, Mohamed, Kos, Zuzana, van Diest, Paul J., Verbandt, Sara, Thagaard, Jeppe, Khiroya, Reena, Abduljabbar, Khalid, Acosta Haab, Gabriela, Acs, Balazs, Adams, Sylvia, Almeida, Jonas S., Alvarado-Cabrero, Isabel, Azmoudeh-Ardalan, Farid, Badve, Sunil, Baharun, Nurkhairul Bariyah, Bellolio, Enrique R., Bheemaraju, Vydehi, Blenman, Kim R.M., Botinelly Mendonça Fujimoto, Luciana, Burgues, Octavio, Chardas, Alexandros, Cheang, Maggie Chon U., Ciompi, Francesco, Cooper, Lee A.D., Coosemans, An, Corredor, Germán, Dantas Portela, Flavio Luis, Deman, Frederik, Demaria, Sandra, Dudgeon, Sarah N., Elghazawy, Mahmoud, Fernandez-Martín, Claudio, Fineberg, Susan, Fox, Stephen B., Giltnane, Jennifer M., Gnjatic, Sacha, Gonzalez-Ericsson, Paula I., Grigoriadis, Anita, Halama, Niels, Hanna, Matthew G., Harbhajanka, Aparna, Hart, Steven N., Hartman, Johan, Hewitt, Stephen, Horlings, Hugo M., Husain, Zaheed, Irshad, Sheeba, Janssen, Emiel A.M., Kataoka, Tatsuki R., Kawaguchi, Kosuke, Khramtsov, Andrey I., Kiraz, Umay, Kirtani, Pawan, Kodach, Liudmila L., Korski, Konstanty, Akturk, Guray, Scott, Ely, Kovács, Anikó, Lænkholm, Anne Vibeke, Lang-Schwarz, Corinna, Larsimont, Denis, Lennerz, Jochen K., Lerousseau, Marvin, Li, Xiaoxian, Madabhushi, Anant, Maley, Sai K., Manur Narasimhamurthy, Vidya, Marks, Douglas K., McDonald, Elizabeth S., Mehrotra, Ravi, Michiels, Stefan, Kharidehal, Durga, Minhas, Fayyaz ul Amir Afsar, Mittal, Shachi, Moore, David A., Mushtaq, Shamim, Nighat, Hussain, Papathomas, Thomas, Penault-Llorca, Frederique, Perera, Rashindrie D., Pinard, Christopher J., Pinto-Cardenas, Juan Carlos, Pruneri, Giancarlo, Pusztai, Lajos, Rajpoot, Nasir Mahmood, Rapoport, Bernardo Leon, Rau, Tilman T., Ribeiro, Joana M., Rimm, David, Vincent-Salomon, Anne, Saltz, Joel, Sayed, Shahin, Hytopoulos, Evangelos, Mahon, Sarah, Siziopikou, Kalliopi P., Sotiriou, Christos, Stenzinger, Albrecht, Sughayer, Maher A., Sur, Daniel, Symmans, Fraser, Tanaka, Sunao, Taxter, Timothy, Tejpar, Sabine, Teuwen, Jonas, Thompson, E. Aubrey, Tramm, Trine, Tran, William T., van der Laak, Jeroen, Verghese, Gregory E., Viale, Giuseppe, Wahab, Noorul, Walter, Thomas, Waumans, Yannick, Wen, Hannah Y., Yang, Wentao, Yuan, Yinyin, Bartlett, John, Loibl, Sibylle, Denkert, Carsten, Savas, Peter, Loi, Sherene, Specht Stovgaard, Elisabeth, Salgado, Roberto, Gallagher, William M., and Rahman, Arman

Abstract

Recent advances in the field of immuno-oncology have brought transformative changes in the management of cancer patients. The immune profile of tumours has been found to have key value in predicting disease prognosis and treatment response in various cancers. Multiplex immunohistochemistry and immunofluorescence have emerged as potent tools for the simultaneous detection of multiple protein biomarkers in a single tissue section, thereby expanding opportunities for molecular and immune profiling while preserving tissue samples. By establishing the phenotype of individual tumour cells when distributed within a mixed cell population, the identification of clinically relevant biomarkers with high-throughput multiplex immunophenotyping of tumour samples has great potential to guide appropriate treatment choices. Moreover, the emergence of novel multi-marker imaging approaches can now provide unprecedented insights into the tumour microenvironment, including the potential interplay between various cell types. However, there are significant challenges to widespread integration of these technologies in daily research and clinical practice. This review addresses the challenges and potential solutions within a structured framework of action from a regulatory and clinical trial perspective. New developments within the field of immunophenotyping using multiplexed tissue imaging platforms and associated digital pathology are also described, with a specific focus on translational implications across different subtypes of cancer.

Published
2024

11. Unveiling the oncogenic role of LZTS1 in colorectal cancer.

Author

Xu, Yuanchun, Pepe, Daniele, Yao, Shu, Boudhan, Loubna, Verbandt, Sara, Pu, Ting, Creemers, John W. M., Liu, Maoxuan, Tejpar, Sabine, He, Zongsheng, Zhu, Jingjing, and Wang, Yaling

Subjects
LEUCINE zippers, COLORECTAL cancer, FUNCTIONAL analysis, CELL migration, CELL proliferation
Abstract

Although leucine zipper tumour suppressor 1 (LZTS1) has been considered a potential tumour suppressor, accumulating evidence suggests that LZTS1 is highly expressed in many cancer types. To unravel the exact role of LZTS1 in colorectal carcinogenesis, we performed the bioinformatic analysis of LZTS1, including expression differences, correlations between expression levels and survival, methylation status of LZTS1 promoter and related cellular pathways based on TCGA dataset, GEO databases and our own CRC patient cohort. Furthermore, we confirmed the oncogenic function of LZTS1 in human mammalian cells by employing a series of assays including tissue microarray, immunoblotting, cell proliferation and migration assay. We found that the expression of LZTS1 is higher in tumour samples compared to paired normal tissue in CRC cancer and its different clinical subtypes, which is, at least in part, due to the low methylation status of LZTS1 promoter in CRC tumour samples. Functional analysis identified the close relationship between high expression of LZTS1 and PI3K‐AKT pathway and the epithelial–mesenchymal transition (EMT) process. Consistently, we found that the expression of LZTS1 positively correlated with the expression PIK3CD, N‐cadherin in CRC tumour samples, while the expression of LZTS1 negatively correlated with the expression of E‐cadherin and PTEN in CRC tumour samples. Experimental data further confirmed that overexpression of LZTS1 upregulated activity of AKT and promoted EMT process. Furthermore, depletion of LZTS1 repressed the proliferation and migration rate of CRC cells. Thus, this study indicates that LZTS1 plays an oncogenic role in colorectal carcinogenesis. [ABSTRACT FROM AUTHOR]

Published
2024
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12. Image‐based multiplex immune profiling of cancer tissues: translational implications. A report of the International Immuno‐oncology Biomarker Working Group on Breast Cancer

Author

Jahangir, Chowdhury Arif, primary, Page, David B, additional, Broeckx, Glenn, additional, Gonzalez, Claudia A, additional, Burke, Caoimbhe, additional, Murphy, Clodagh, additional, Reis‐Filho, Jorge S, additional, Ly, Amy, additional, Harms, Paul W, additional, Gupta, Rajarsi R, additional, Vieth, Michael, additional, Hida, Akira I, additional, Kahila, Mohamed, additional, Kos, Zuzana, additional, van Diest, Paul J, additional, Verbandt, Sara, additional, Thagaard, Jeppe, additional, Khiroya, Reena, additional, Abduljabbar, Khalid, additional, Acosta Haab, Gabriela, additional, Acs, Balazs, additional, Adams, Sylvia, additional, Almeida, Jonas S, additional, Alvarado‐Cabrero, Isabel, additional, Azmoudeh‐Ardalan, Farid, additional, Badve, Sunil, additional, Baharun, Nurkhairul Bariyah, additional, Bellolio, Enrique R, additional, Bheemaraju, Vydehi, additional, Blenman, Kim RM, additional, Botinelly Mendonça Fujimoto, Luciana, additional, Burgues, Octavio, additional, Chardas, Alexandros, additional, Cheang, Maggie Chon U, additional, Ciompi, Francesco, additional, Cooper, Lee AD, additional, Coosemans, An, additional, Corredor, Germán, additional, Dantas Portela, Flavio Luis, additional, Deman, Frederik, additional, Demaria, Sandra, additional, Dudgeon, Sarah N, additional, Elghazawy, Mahmoud, additional, Fernandez‐Martín, Claudio, additional, Fineberg, Susan, additional, Fox, Stephen B, additional, Giltnane, Jennifer M, additional, Gnjatic, Sacha, additional, Gonzalez‐Ericsson, Paula I, additional, Grigoriadis, Anita, additional, Halama, Niels, additional, Hanna, Matthew G, additional, Harbhajanka, Aparna, additional, Hart, Steven N, additional, Hartman, Johan, additional, Hewitt, Stephen, additional, Horlings, Hugo M, additional, Husain, Zaheed, additional, Irshad, Sheeba, additional, Janssen, Emiel AM, additional, Kataoka, Tatsuki R, additional, Kawaguchi, Kosuke, additional, Khramtsov, Andrey I, additional, Kiraz, Umay, additional, Kirtani, Pawan, additional, Kodach, Liudmila L, additional, Korski, Konstanty, additional, Akturk, Guray, additional, Scott, Ely, additional, Kovács, Anikó, additional, Lænkholm, Anne‐Vibeke, additional, Lang‐Schwarz, Corinna, additional, Larsimont, Denis, additional, Lennerz, Jochen K, additional, Lerousseau, Marvin, additional, Li, Xiaoxian, additional, Madabhushi, Anant, additional, Maley, Sai K, additional, Manur Narasimhamurthy, Vidya, additional, Marks, Douglas K, additional, McDonald, Elizabeth S, additional, Mehrotra, Ravi, additional, Michiels, Stefan, additional, Kharidehal, Durga, additional, Minhas, Fayyaz ul Amir Afsar, additional, Mittal, Shachi, additional, Moore, David A, additional, Mushtaq, Shamim, additional, Nighat, Hussain, additional, Papathomas, Thomas, additional, Penault‐Llorca, Frederique, additional, Perera, Rashindrie D, additional, Pinard, Christopher J, additional, Pinto‐Cardenas, Juan Carlos, additional, Pruneri, Giancarlo, additional, Pusztai, Lajos, additional, Rajpoot, Nasir Mahmood, additional, Rapoport, Bernardo Leon, additional, Rau, Tilman T, additional, Ribeiro, Joana M, additional, Rimm, David, additional, Vincent‐Salomon, Anne, additional, Saltz, Joel, additional, Sayed, Shahin, additional, Hytopoulos, Evangelos, additional, Mahon, Sarah, additional, Siziopikou, Kalliopi P, additional, Sotiriou, Christos, additional, Stenzinger, Albrecht, additional, Sughayer, Maher A, additional, Sur, Daniel, additional, Symmans, Fraser, additional, Tanaka, Sunao, additional, Taxter, Timothy, additional, Tejpar, Sabine, additional, Teuwen, Jonas, additional, Thompson, E Aubrey, additional, Tramm, Trine, additional, Tran, William T, additional, van der Laak, Jeroen, additional, Verghese, Gregory E, additional, Viale, Giuseppe, additional, Wahab, Noorul, additional, Walter, Thomas, additional, Waumans, Yannick, additional, Wen, Hannah Y, additional, Yang, Wentao, additional, Yuan, Yinyin, additional, Bartlett, John, additional, Loibl, Sibylle, additional, Denkert, Carsten, additional, Savas, Peter, additional, Loi, Sherene, additional, Specht Stovgaard, Elisabeth, additional, Salgado, Roberto, additional, Gallagher, William M, additional, and Rahman, Arman, additional

Published
2024
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13. A pan-cancer blueprint of the heterogeneous tumor microenvironment revealed by single-cell profiling

Author

Qian, Junbin, Olbrecht, Siel, Boeckx, Bram, Vos, Hanne, Laoui, Damya, Etlioglu, Emre, Wauters, Els, Pomella, Valentina, Verbandt, Sara, Busschaert, Pieter, Bassez, Ayse, Franken, Amelie, Bempt, Marlies Vanden, Xiong, Jieyi, Weynand, Birgit, van Herck, Yannick, Antoranz, Asier, Bosisio, Francesca Maria, Thienpont, Bernard, Floris, Giuseppe, Vergote, Ignace, Smeets, Ann, Tejpar, Sabine, and Lambrechts, Diether

Published
2020
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14. Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer

Author

Lee, Hae-Ock, Hong, Yourae, Etlioglu, Hakki Emre, Cho, Yong Beom, Pomella, Valentina, Van den Bosch, Ben, Vanhecke, Jasper, Verbandt, Sara, Hong, Hyekyung, Min, Jae-Woong, Kim, Nayoung, Eum, Hye Hyeon, Qian, Junbin, Boeckx, Bram, Lambrechts, Diether, Tsantoulis, Petros, De Hertogh, Gert, Chung, Woosung, Lee, Taeseob, An, Minae, Shin, Hyun-Tae, Joung, Je-Gun, Jung, Min-Hyeok, Ko, Gunhwan, Wirapati, Pratyaksha, Kim, Seok Hyung, Kim, Hee Cheol, Yun, Seong Hyeon, Tan, Iain Bee Huat, Ranjan, Bobby, Lee, Woo Yong, Kim, Tae-You, Choi, Jung Kyoon, Kim, Young-Joon, Prabhakar, Shyam, Tejpar, Sabine, and Park, Woong-Yang

Published
2020
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15. Spatial analyses of immune cell infiltration in cancer: current methods and future directions. A report of the International Immuno‐Oncology Biomarker Working Group on Breast Cancer

Author

Page, David B, primary, Broeckx, Glenn, additional, Jahangir, Chowdhury Arif, additional, Verbandt, Sara, additional, Gupta, Rajarsi R, additional, Thagaard, Jeppe, additional, Khiroya, Reena, additional, Kos, Zuzana, additional, Abduljabbar, Khalid, additional, Acosta Haab, Gabriela, additional, Acs, Balazs, additional, Almeida, Jonas S, additional, Alvarado‐Cabrero, Isabel, additional, Azmoudeh‐Ardalan, Farid, additional, Badve, Sunil, additional, Baharun, Nurkhairul Bariyah, additional, Bellolio, Enrique R, additional, Bheemaraju, Vydehi, additional, Blenman, Kim RM, additional, Botinelly Mendonça Fujimoto, Luciana, additional, Burgues, Octavio, additional, Cheang, Maggie Chon U, additional, Ciompi, Francesco, additional, Cooper, Lee AD, additional, Coosemans, An, additional, Corredor, Germán, additional, Dantas Portela, Flavio Luis, additional, Deman, Frederik, additional, Demaria, Sandra, additional, Dudgeon, Sarah N, additional, Elghazawy, Mahmoud, additional, Ely, Scott, additional, Fernandez‐Martín, Claudio, additional, Fineberg, Susan, additional, Fox, Stephen B, additional, Gallagher, William M, additional, Giltnane, Jennifer M, additional, Gnjatic, Sacha, additional, Gonzalez‐Ericsson, Paula I, additional, Grigoriadis, Anita, additional, Halama, Niels, additional, Hanna, Matthew G, additional, Harbhajanka, Aparna, additional, Hardas, Alexandros, additional, Hart, Steven N, additional, Hartman, Johan, additional, Hewitt, Stephen, additional, Hida, Akira I, additional, Horlings, Hugo M, additional, Husain, Zaheed, additional, Hytopoulos, Evangelos, additional, Irshad, Sheeba, additional, Janssen, Emiel AM, additional, Kahila, Mohamed, additional, Kataoka, Tatsuki R, additional, Kawaguchi, Kosuke, additional, Kharidehal, Durga, additional, Khramtsov, Andrey I, additional, Kiraz, Umay, additional, Kirtani, Pawan, additional, Kodach, Liudmila L, additional, Korski, Konstanty, additional, Kovács, Anikó, additional, Laenkholm, Anne‐Vibeke, additional, Lang‐Schwarz, Corinna, additional, Larsimont, Denis, additional, Lennerz, Jochen K, additional, Lerousseau, Marvin, additional, Li, Xiaoxian, additional, Ly, Amy, additional, Madabhushi, Anant, additional, Maley, Sai K, additional, Manur Narasimhamurthy, Vidya, additional, Marks, Douglas K, additional, McDonald, Elizabeth S, additional, Mehrotra, Ravi, additional, Michiels, Stefan, additional, Minhas, Fayyaz ul Amir Afsar, additional, Mittal, Shachi, additional, Moore, David A, additional, Mushtaq, Shamim, additional, Nighat, Hussain, additional, Papathomas, Thomas, additional, Penault‐Llorca, Frederique, additional, Perera, Rashindrie D, additional, Pinard, Christopher J, additional, Pinto‐Cardenas, Juan Carlos, additional, Pruneri, Giancarlo, additional, Pusztai, Lajos, additional, Rahman, Arman, additional, Rajpoot, Nasir Mahmood, additional, Rapoport, Bernardo Leon, additional, Rau, Tilman T, additional, Reis‐Filho, Jorge S, additional, Ribeiro, Joana M, additional, Rimm, David, additional, Salomon, Anne‐Vincent, additional, Salto‐Tellez, Manuel, additional, Saltz, Joel, additional, Sayed, Shahin, additional, Siziopikou, Kalliopi P, additional, Sotiriou, Christos, additional, Stenzinger, Albrecht, additional, Sughayer, Maher A, additional, Sur, Daniel, additional, Symmans, Fraser, additional, Tanaka, Sunao, additional, Taxter, Timothy, additional, Tejpar, Sabine, additional, Teuwen, Jonas, additional, Thompson, E Aubrey, additional, Tramm, Trine, additional, Tran, William T, additional, van der Laak, Jeroen, additional, van Diest, Paul J, additional, Verghese, Gregory E, additional, Viale, Giuseppe, additional, Vieth, Michael, additional, Wahab, Noorul, additional, Walter, Thomas, additional, Waumans, Yannick, additional, Wen, Hannah Y, additional, Yang, Wentao, additional, Yuan, Yinyin, additional, Adams, Sylvia, additional, Bartlett, John Mark Seaverns, additional, Loibl, Sibylle, additional, Denkert, Carsten, additional, Savas, Peter, additional, Loi, Sherene, additional, Salgado, Roberto, additional, Specht Stovgaard, Elisabeth, additional, Akturk, Guray, additional, and Bouchmaa, Najat, additional

Published
2023
Full Text
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16. Pitfalls in machine learning‐based assessment of tumor‐infiltrating lymphocytes in breast cancer: a report of the international immuno‐oncology biomarker working group

Author

Thagaard, Jeppe, primary, Broeckx, Glenn, additional, Page, David B, additional, Jahangir, Chowdhury Arif, additional, Verbandt, Sara, additional, Kos, Zuzana, additional, Gupta, Rajarsi, additional, Khiroya, Reena, additional, Abduljabbar, Khalid, additional, Acosta Haab, Gabriela, additional, Acs, Balazs, additional, Akturk, Guray, additional, Almeida, Jonas S, additional, Alvarado‐Cabrero, Isabel, additional, Amgad, Mohamed, additional, Azmoudeh‐Ardalan, Farid, additional, Badve, Sunil, additional, Baharun, Nurkhairul Bariyah, additional, Balslev, Eva, additional, Bellolio, Enrique R, additional, Bheemaraju, Vydehi, additional, Blenman, Kim RM, additional, Botinelly Mendonça Fujimoto, Luciana, additional, Bouchmaa, Najat, additional, Burgues, Octavio, additional, Chardas, Alexandros, additional, Chon U Cheang, Maggie, additional, Ciompi, Francesco, additional, Cooper, Lee AD, additional, Coosemans, An, additional, Corredor, Germán, additional, Dahl, Anders B, additional, Dantas Portela, Flavio Luis, additional, Deman, Frederik, additional, Demaria, Sandra, additional, Doré Hansen, Johan, additional, Dudgeon, Sarah N, additional, Ebstrup, Thomas, additional, Elghazawy, Mahmoud, additional, Fernandez‐Martín, Claudio, additional, Fox, Stephen B, additional, Gallagher, William M, additional, Giltnane, Jennifer M, additional, Gnjatic, Sacha, additional, Gonzalez‐Ericsson, Paula I, additional, Grigoriadis, Anita, additional, Halama, Niels, additional, Hanna, Matthew G, additional, Harbhajanka, Aparna, additional, Hart, Steven N, additional, Hartman, Johan, additional, Hauberg, Søren, additional, Hewitt, Stephen, additional, Hida, Akira I, additional, Horlings, Hugo M, additional, Husain, Zaheed, additional, Hytopoulos, Evangelos, additional, Irshad, Sheeba, additional, Janssen, Emiel AM, additional, Kahila, Mohamed, additional, Kataoka, Tatsuki R, additional, Kawaguchi, Kosuke, additional, Kharidehal, Durga, additional, Khramtsov, Andrey I, additional, Kiraz, Umay, additional, Kirtani, Pawan, additional, Kodach, Liudmila L, additional, Korski, Konstanty, additional, Kovács, Anikó, additional, Laenkholm, Anne‐Vibeke, additional, Lang‐Schwarz, Corinna, additional, Larsimont, Denis, additional, Lennerz, Jochen K, additional, Lerousseau, Marvin, additional, Li, Xiaoxian, additional, Ly, Amy, additional, Madabhushi, Anant, additional, Maley, Sai K, additional, Manur Narasimhamurthy, Vidya, additional, Marks, Douglas K, additional, McDonald, Elizabeth S, additional, Mehrotra, Ravi, additional, Michiels, Stefan, additional, Minhas, Fayyaz ul Amir Afsar, additional, Mittal, Shachi, additional, Moore, David A, additional, Mushtaq, Shamim, additional, Nighat, Hussain, additional, Papathomas, Thomas, additional, Penault‐Llorca, Frederique, additional, Perera, Rashindrie D, additional, Pinard, Christopher J, additional, Pinto‐Cardenas, Juan Carlos, additional, Pruneri, Giancarlo, additional, Pusztai, Lajos, additional, Rahman, Arman, additional, Rajpoot, Nasir Mahmood, additional, Rapoport, Bernardo Leon, additional, Rau, Tilman T, additional, Reis‐Filho, Jorge S, additional, Ribeiro, Joana M, additional, Rimm, David, additional, Roslind, Anne, additional, Vincent‐Salomon, Anne, additional, Salto‐Tellez, Manuel, additional, Saltz, Joel, additional, Sayed, Shahin, additional, Scott, Ely, additional, Siziopikou, Kalliopi P, additional, Sotiriou, Christos, additional, Stenzinger, Albrecht, additional, Sughayer, Maher A, additional, Sur, Daniel, additional, Fineberg, Susan, additional, Symmans, Fraser, additional, Tanaka, Sunao, additional, Taxter, Timothy, additional, Tejpar, Sabine, additional, Teuwen, Jonas, additional, Thompson, E Aubrey, additional, Tramm, Trine, additional, Tran, William T, additional, van der Laak, Jeroen, additional, van Diest, Paul J, additional, Verghese, Gregory E, additional, Viale, Giuseppe, additional, Vieth, Michael, additional, Wahab, Noorul, additional, Walter, Thomas, additional, Waumans, Yannick, additional, Wen, Hannah Y, additional, Yang, Wentao, additional, Yuan, Yinyin, additional, Zin, Reena Md, additional, Adams, Sylvia, additional, Bartlett, John, additional, Loibl, Sibylle, additional, Denkert, Carsten, additional, Savas, Peter, additional, Loi, Sherene, additional, Salgado, Roberto, additional, and Specht Stovgaard, Elisabeth, additional

Published
2023
Full Text
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17. IL-1R signaling drives enteric glia-macrophage interaction in colorectal cancer progression

Author

van Baarle, Lies, primary, De Simone, Veronica, additional, Schneider, Linda, additional, Santhosh, Sneha, additional, Abdurahiman, Saeed, additional, Biscu, Francesca, additional, Schneider, Reiner, additional, Zanoletti, Lisa, additional, Verbandt, Sara, additional, Hu, Zedong, additional, Stakenborg, Michelle, additional, Ke, Bo-Jun, additional, Garcia-Reyes, Balbina, additional, Henn, Jonas, additional, Toma, Marieta, additional, Vanmechelen, Maxime, additional, De Smet, Frederik, additional, Ibiza, Sales, additional, Tejpar, Sabine, additional, Wehner, Sven, additional, and Matteoli, Gianluca, additional

Published
2023
Full Text
View/download PDF

18. Pitfalls in machine learning-based assessment of tumor-infiltrating lymphocytes in breast cancer:A report of the International Immuno-Oncology Biomarker Working Group on Breast Cancer

Author

Thagaard, Jeppe, Broeckx, Glenn, Page, David B, Jahangir, Chowdhury Arif, Verbandt, Sara, Kos, Zuzana, Gupta, Rajarsi, Khiroya, Reena, Abduljabbar, Khalid, Acosta Haab, Gabriela, Acs, Balazs, Akturk, Guray, Almeida, Jonas S, Alvarado-Cabrero, Isabel, Amgad, Mohamed, Azmoudeh-Ardalan, Farid, Badve, Sunil, Baharun, Nurkhairul Bariyah, Balslev, Eva, Bellolio, Enrique R, Bheemaraju, Vydehi, Blenman, Kim Rm, Botinelly Mendonça Fujimoto, Luciana, Bouchmaa, Najat, Burgues, Octavio, Chardas, Alexandros, Chon U Cheang, Maggie, Ciompi, Francesco, Cooper, Lee Ad, Coosemans, An, Corredor, Germán, Dahl, Anders B, Dantas Portela, Flavio Luis, Deman, Frederik, Demaria, Sandra, Doré Hansen, Johan, Dudgeon, Sarah N, Ebstrup, Thomas, Elghazawy, Mahmoud, Fernandez-Martín, Claudio, Fox, Stephen B, Gallagher, William M, Giltnane, Jennifer M, Gnjatic, Sacha, Gonzalez-Ericsson, Paula I, Grigoriadis, Anita, Halama, Niels, Hanna, Matthew G, Harbhajanka, Aparna, Hart, Steven N, Hartman, Johan, Hauberg, Søren, Hewitt, Stephen, Hida, Akira I, Horlings, Hugo M, Husain, Zaheed, Hytopoulos, Evangelos, Irshad, Sheeba, Janssen, Emiel Am, Kahila, Mohamed, Kataoka, Tatsuki R, Kawaguchi, Kosuke, Kharidehal, Durga, Khramtsov, Andrey I, Kiraz, Umay, Kirtani, Pawan, Kodach, Liudmila L, Korski, Konstanty, Kovács, Anikó, Laenkholm, Anne-Vibeke, Lang-Schwarz, Corinna, Larsimont, Denis, Lennerz, Jochen K, Lerousseau, Marvin, Li, Xiaoxian, Ly, Amy, Madabhushi, Anant, Maley, Sai K, Manur Narasimhamurthy, Vidya, Marks, Douglas K, McDonald, Elizabeth S, Mehrotra, Ravi, Michiels, Stefan, Minhas, Fayyaz Ul Amir Afsar, Mittal, Shachi, Moore, David A, Mushtaq, Shamim, Nighat, Hussain, Papathomas, Thomas, Penault-Llorca, Frederique, Perera, Rashindrie D, Pinard, Christopher J, Pinto-Cardenas, Juan Carlos, Pruneri, Giancarlo, Pusztai, Lajos, Rahman, Arman, Rajpoot, Nasir Mahmood, Rapoport, Bernardo Leon, Rau, Tilman T, Reis-Filho, Jorge S, Ribeiro, Joana M, Rimm, David, Roslind, Anne, Vincent-Salomon, Anne, Salto-Tellez, Manuel, Saltz, Joel, Sayed, Shahin, Scott, Ely, Siziopikou, Kalliopi P, Sotiriou, Christos, Stenzinger, Albrecht, Sughayer, Maher A, Sur, Daniel, Fineberg, Susan, Symmans, Fraser, Tanaka, Sunao, Taxter, Timothy, Tejpar, Sabine, Teuwen, Jonas, Thompson, E Aubrey, Tramm, Trine, Tran, William T, van der Laak, Jeroen, van Diest, Paul J, Verghese, Gregory E, Viale, Giuseppe, Vieth, Michael, Wahab, Noorul, Walter, Thomas, Waumans, Yannick, Wen, Hannah Y, Yang, Wentao, Yuan, Yinyin, Zin, Reena Md, Adams, Sylvia, Bartlett, John, Loibl, Sibylle, Denkert, Carsten, Savas, Peter, Loi, Sherene, Salgado, Roberto, Specht Stovgaard, Elisabeth, Thagaard, Jeppe, Broeckx, Glenn, Page, David B, Jahangir, Chowdhury Arif, Verbandt, Sara, Kos, Zuzana, Gupta, Rajarsi, Khiroya, Reena, Abduljabbar, Khalid, Acosta Haab, Gabriela, Acs, Balazs, Akturk, Guray, Almeida, Jonas S, Alvarado-Cabrero, Isabel, Amgad, Mohamed, Azmoudeh-Ardalan, Farid, Badve, Sunil, Baharun, Nurkhairul Bariyah, Balslev, Eva, Bellolio, Enrique R, Bheemaraju, Vydehi, Blenman, Kim Rm, Botinelly Mendonça Fujimoto, Luciana, Bouchmaa, Najat, Burgues, Octavio, Chardas, Alexandros, Chon U Cheang, Maggie, Ciompi, Francesco, Cooper, Lee Ad, Coosemans, An, Corredor, Germán, Dahl, Anders B, Dantas Portela, Flavio Luis, Deman, Frederik, Demaria, Sandra, Doré Hansen, Johan, Dudgeon, Sarah N, Ebstrup, Thomas, Elghazawy, Mahmoud, Fernandez-Martín, Claudio, Fox, Stephen B, Gallagher, William M, Giltnane, Jennifer M, Gnjatic, Sacha, Gonzalez-Ericsson, Paula I, Grigoriadis, Anita, Halama, Niels, Hanna, Matthew G, Harbhajanka, Aparna, Hart, Steven N, Hartman, Johan, Hauberg, Søren, Hewitt, Stephen, Hida, Akira I, Horlings, Hugo M, Husain, Zaheed, Hytopoulos, Evangelos, Irshad, Sheeba, Janssen, Emiel Am, Kahila, Mohamed, Kataoka, Tatsuki R, Kawaguchi, Kosuke, Kharidehal, Durga, Khramtsov, Andrey I, Kiraz, Umay, Kirtani, Pawan, Kodach, Liudmila L, Korski, Konstanty, Kovács, Anikó, Laenkholm, Anne-Vibeke, Lang-Schwarz, Corinna, Larsimont, Denis, Lennerz, Jochen K, Lerousseau, Marvin, Li, Xiaoxian, Ly, Amy, Madabhushi, Anant, Maley, Sai K, Manur Narasimhamurthy, Vidya, Marks, Douglas K, McDonald, Elizabeth S, Mehrotra, Ravi, Michiels, Stefan, Minhas, Fayyaz Ul Amir Afsar, Mittal, Shachi, Moore, David A, Mushtaq, Shamim, Nighat, Hussain, Papathomas, Thomas, Penault-Llorca, Frederique, Perera, Rashindrie D, Pinard, Christopher J, Pinto-Cardenas, Juan Carlos, Pruneri, Giancarlo, Pusztai, Lajos, Rahman, Arman, Rajpoot, Nasir Mahmood, Rapoport, Bernardo Leon, Rau, Tilman T, Reis-Filho, Jorge S, Ribeiro, Joana M, Rimm, David, Roslind, Anne, Vincent-Salomon, Anne, Salto-Tellez, Manuel, Saltz, Joel, Sayed, Shahin, Scott, Ely, Siziopikou, Kalliopi P, Sotiriou, Christos, Stenzinger, Albrecht, Sughayer, Maher A, Sur, Daniel, Fineberg, Susan, Symmans, Fraser, Tanaka, Sunao, Taxter, Timothy, Tejpar, Sabine, Teuwen, Jonas, Thompson, E Aubrey, Tramm, Trine, Tran, William T, van der Laak, Jeroen, van Diest, Paul J, Verghese, Gregory E, Viale, Giuseppe, Vieth, Michael, Wahab, Noorul, Walter, Thomas, Waumans, Yannick, Wen, Hannah Y, Yang, Wentao, Yuan, Yinyin, Zin, Reena Md, Adams, Sylvia, Bartlett, John, Loibl, Sibylle, Denkert, Carsten, Savas, Peter, Loi, Sherene, Salgado, Roberto, and Specht Stovgaard, Elisabeth

Abstract

The clinical significance of the tumor-immune interaction in breast cancer is now established, and tumor-infiltrating lymphocytes (TILs) have emerged as predictive and prognostic biomarkers for patients with triple-negative (estrogen receptor, progesterone receptor, and HER2-negative) breast cancer and HER2-positive breast cancer. How computational assessments of TILs might complement manual TIL assessment in trial and daily practices is currently debated. Recent efforts to use machine learning (ML) to automatically evaluate TILs have shown promising results. We review state-of-the-art approaches and identify pitfalls and challenges of automated TIL evaluation by studying the root cause of ML discordances in comparison to manual TIL quantification. We categorize our findings into four main topics: (1) technical slide issues, (2) ML and image analysis aspects, (3) data challenges, and (4) validation issues. The main reason for discordant assessments is the inclusion of false-positive areas or cells identified by performance on certain tissue patterns or design choices in the computational implementation. To aid the adoption of ML for TIL assessment, we provide an in-depth discussion of ML and image analysis, including validation issues that need to be considered before reliable computational reporting of TILs can be incorporated into the trial and routine clinical management of patients with triple-negative breast cancer.

Published
2023

19. Pitfalls in machine learning-based assessment of tumor-infiltrating lymphocytes in breast cancer: A report of the International Immuno-Oncology Biomarker Working Group on Breast Cancer

Author

Pathologie, Cancer, Thagaard, Jeppe, Broeckx, Glenn, Page, David B, Jahangir, Chowdhury Arif, Verbandt, Sara, Kos, Zuzana, Gupta, Rajarsi, Khiroya, Reena, Abduljabbar, Khalid, Acosta Haab, Gabriela, Acs, Balazs, Akturk, Guray, Almeida, Jonas S, Alvarado-Cabrero, Isabel, Amgad, Mohamed, Azmoudeh-Ardalan, Farid, Badve, Sunil, Baharun, Nurkhairul Bariyah, Balslev, Eva, Bellolio, Enrique R, Bheemaraju, Vydehi, Blenman, Kim Rm, Botinelly Mendonça Fujimoto, Luciana, Bouchmaa, Najat, Burgues, Octavio, Chardas, Alexandros, Chon U Cheang, Maggie, Ciompi, Francesco, Cooper, Lee Ad, Coosemans, An, Corredor, Germán, Dahl, Anders B, Dantas Portela, Flavio Luis, Deman, Frederik, Demaria, Sandra, Doré Hansen, Johan, Dudgeon, Sarah N, Ebstrup, Thomas, Elghazawy, Mahmoud, Fernandez-Martín, Claudio, Fox, Stephen B, Gallagher, William M, Giltnane, Jennifer M, Gnjatic, Sacha, Gonzalez-Ericsson, Paula I, Grigoriadis, Anita, Halama, Niels, Hanna, Matthew G, Harbhajanka, Aparna, Hart, Steven N, Hartman, Johan, Hauberg, Søren, Hewitt, Stephen, Hida, Akira I, Horlings, Hugo M, Husain, Zaheed, Hytopoulos, Evangelos, Irshad, Sheeba, Janssen, Emiel Am, Kahila, Mohamed, Kataoka, Tatsuki R, Kawaguchi, Kosuke, Kharidehal, Durga, Khramtsov, Andrey I, Kiraz, Umay, Kirtani, Pawan, Kodach, Liudmila L, Korski, Konstanty, Kovács, Anikó, Laenkholm, Anne-Vibeke, Lang-Schwarz, Corinna, Larsimont, Denis, Lennerz, Jochen K, Lerousseau, Marvin, Li, Xiaoxian, Ly, Amy, Madabhushi, Anant, Maley, Sai K, Manur Narasimhamurthy, Vidya, Marks, Douglas K, McDonald, Elizabeth S, Mehrotra, Ravi, Michiels, Stefan, Minhas, Fayyaz Ul Amir Afsar, Mittal, Shachi, Moore, David A, Mushtaq, Shamim, Nighat, Hussain, Papathomas, Thomas, Penault-Llorca, Frederique, Perera, Rashindrie D, Pinard, Christopher J, Pinto-Cardenas, Juan Carlos, Pruneri, Giancarlo, Pusztai, Lajos, Rahman, Arman, Rajpoot, Nasir Mahmood, Rapoport, Bernardo Leon, Rau, Tilman T, Reis-Filho, Jorge S, Ribeiro, Joana M, Rimm, David, Roslind, Anne, Vincent-Salomon, Anne, Salto-Tellez, Manuel, Saltz, Joel, Sayed, Shahin, Scott, Ely, Siziopikou, Kalliopi P, Sotiriou, Christos, Stenzinger, Albrecht, Sughayer, Maher A, Sur, Daniel, Fineberg, Susan, Symmans, Fraser, Tanaka, Sunao, Taxter, Timothy, Tejpar, Sabine, Teuwen, Jonas, Thompson, E Aubrey, Tramm, Trine, Tran, William T, van der Laak, Jeroen, van Diest, Paul J, Verghese, Gregory E, Viale, Giuseppe, Vieth, Michael, Wahab, Noorul, Walter, Thomas, Waumans, Yannick, Wen, Hannah Y, Yang, Wentao, Yuan, Yinyin, Zin, Reena Md, Adams, Sylvia, Bartlett, John, Loibl, Sibylle, Denkert, Carsten, Savas, Peter, Loi, Sherene, Salgado, Roberto, Specht Stovgaard, Elisabeth, Pathologie, Cancer, Thagaard, Jeppe, Broeckx, Glenn, Page, David B, Jahangir, Chowdhury Arif, Verbandt, Sara, Kos, Zuzana, Gupta, Rajarsi, Khiroya, Reena, Abduljabbar, Khalid, Acosta Haab, Gabriela, Acs, Balazs, Akturk, Guray, Almeida, Jonas S, Alvarado-Cabrero, Isabel, Amgad, Mohamed, Azmoudeh-Ardalan, Farid, Badve, Sunil, Baharun, Nurkhairul Bariyah, Balslev, Eva, Bellolio, Enrique R, Bheemaraju, Vydehi, Blenman, Kim Rm, Botinelly Mendonça Fujimoto, Luciana, Bouchmaa, Najat, Burgues, Octavio, Chardas, Alexandros, Chon U Cheang, Maggie, Ciompi, Francesco, Cooper, Lee Ad, Coosemans, An, Corredor, Germán, Dahl, Anders B, Dantas Portela, Flavio Luis, Deman, Frederik, Demaria, Sandra, Doré Hansen, Johan, Dudgeon, Sarah N, Ebstrup, Thomas, Elghazawy, Mahmoud, Fernandez-Martín, Claudio, Fox, Stephen B, Gallagher, William M, Giltnane, Jennifer M, Gnjatic, Sacha, Gonzalez-Ericsson, Paula I, Grigoriadis, Anita, Halama, Niels, Hanna, Matthew G, Harbhajanka, Aparna, Hart, Steven N, Hartman, Johan, Hauberg, Søren, Hewitt, Stephen, Hida, Akira I, Horlings, Hugo M, Husain, Zaheed, Hytopoulos, Evangelos, Irshad, Sheeba, Janssen, Emiel Am, Kahila, Mohamed, Kataoka, Tatsuki R, Kawaguchi, Kosuke, Kharidehal, Durga, Khramtsov, Andrey I, Kiraz, Umay, Kirtani, Pawan, Kodach, Liudmila L, Korski, Konstanty, Kovács, Anikó, Laenkholm, Anne-Vibeke, Lang-Schwarz, Corinna, Larsimont, Denis, Lennerz, Jochen K, Lerousseau, Marvin, Li, Xiaoxian, Ly, Amy, Madabhushi, Anant, Maley, Sai K, Manur Narasimhamurthy, Vidya, Marks, Douglas K, McDonald, Elizabeth S, Mehrotra, Ravi, Michiels, Stefan, Minhas, Fayyaz Ul Amir Afsar, Mittal, Shachi, Moore, David A, Mushtaq, Shamim, Nighat, Hussain, Papathomas, Thomas, Penault-Llorca, Frederique, Perera, Rashindrie D, Pinard, Christopher J, Pinto-Cardenas, Juan Carlos, Pruneri, Giancarlo, Pusztai, Lajos, Rahman, Arman, Rajpoot, Nasir Mahmood, Rapoport, Bernardo Leon, Rau, Tilman T, Reis-Filho, Jorge S, Ribeiro, Joana M, Rimm, David, Roslind, Anne, Vincent-Salomon, Anne, Salto-Tellez, Manuel, Saltz, Joel, Sayed, Shahin, Scott, Ely, Siziopikou, Kalliopi P, Sotiriou, Christos, Stenzinger, Albrecht, Sughayer, Maher A, Sur, Daniel, Fineberg, Susan, Symmans, Fraser, Tanaka, Sunao, Taxter, Timothy, Tejpar, Sabine, Teuwen, Jonas, Thompson, E Aubrey, Tramm, Trine, Tran, William T, van der Laak, Jeroen, van Diest, Paul J, Verghese, Gregory E, Viale, Giuseppe, Vieth, Michael, Wahab, Noorul, Walter, Thomas, Waumans, Yannick, Wen, Hannah Y, Yang, Wentao, Yuan, Yinyin, Zin, Reena Md, Adams, Sylvia, Bartlett, John, Loibl, Sibylle, Denkert, Carsten, Savas, Peter, Loi, Sherene, Salgado, Roberto, and Specht Stovgaard, Elisabeth

Published
2023

20. Spatial analyses of immune cell infiltration in cancer: current methods and future directions. A report of the International Immuno-Oncology Biomarker Working Group on Breast Cancer

Author

Pathologie, Cancer, Page, David B, Broeckx, Glenn, Jahangir, Chowdhury Arif, Verbandt, Sara, Gupta, Rajarsi R, Thagaard, Jeppe, Khiroya, Reena, Kos, Zuzana, Abduljabbar, Khalid, Acosta Haab, Gabriela, Acs, Balazs, Almeida, Jonas S, Alvarado-Cabrero, Isabel, Azmoudeh-Ardalan, Farid, Badve, Sunil, Baharun, Nurkhairul Bariyah, Bellolio, Enrique R, Bheemaraju, Vydehi, Blenman, Kim Rm, Botinelly Mendonça Fujimoto, Luciana, Burgues, Octavio, Cheang, Maggie Chon U, Ciompi, Francesco, Cooper, Lee Ad, Coosemans, An, Corredor, Germán, Dantas Portela, Flavio Luis, Deman, Frederik, Demaria, Sandra, Dudgeon, Sarah N, Elghazawy, Mahmoud, Ely, Scott, Fernandez-Martín, Claudio, Fineberg, Susan, Fox, Stephen B, Gallagher, William M, Giltnane, Jennifer M, Gnjatic, Sacha, Gonzalez-Ericsson, Paula I, Grigoriadis, Anita, Halama, Niels, Hanna, Matthew G, Harbhajanka, Aparna, Hardas, Alexandros, Hart, Steven N, Hartman, Johan, Hewitt, Stephen, Hida, Akira I, Horlings, Hugo M, Husain, Zaheed, Hytopoulos, Evangelos, Irshad, Sheeba, Janssen, Emiel Am, Kahila, Mohamed, Kataoka, Tatsuki R, Kawaguchi, Kosuke, Kharidehal, Durga, Khramtsov, Andrey I, Kiraz, Umay, Kirtani, Pawan, Kodach, Liudmila L, Korski, Konstanty, Kovács, Anikó, Laenkholm, Anne-Vibeke, Lang-Schwarz, Corinna, Larsimont, Denis, Lennerz, Jochen K, Lerousseau, Marvin, Li, Xiaoxian, Ly, Amy, Madabhushi, Anant, Maley, Sai K, Manur Narasimhamurthy, Vidya, Marks, Douglas K, McDonald, Elizabeth S, Mehrotra, Ravi, Michiels, Stefan, Minhas, Fayyaz Ul Amir Afsar, Mittal, Shachi, Moore, David A, Mushtaq, Shamim, Nighat, Hussain, Papathomas, Thomas, Penault-Llorca, Frederique, Perera, Rashindrie D, Pinard, Christopher J, Pinto-Cardenas, Juan Carlos, Pruneri, Giancarlo, Pusztai, Lajos, Rahman, Arman, Rajpoot, Nasir Mahmood, Rapoport, Bernardo Leon, Rau, Tilman T, Reis-Filho, Jorge S, Ribeiro, Joana M, Rimm, David, Salomon, Anne-Vincent, Salto-Tellez, Manuel, Saltz, Joel, Sayed, Shahin, Siziopikou, Kalliopi P, Sotiriou, Christos, Stenzinger, Albrecht, Sughayer, Maher A, Sur, Daniel, Symmans, Fraser, Tanaka, Sunao, Taxter, Timothy, Tejpar, Sabine, Teuwen, Jonas, Thompson, E Aubrey, Tramm, Trine, Tran, William T, van der Laak, Jeroen, van Diest, Paul J, Verghese, Gregory E, Viale, Giuseppe, Vieth, Michael, Wahab, Noorul, Walter, Thomas, Waumans, Yannick, Wen, Hannah Y, Yang, Wentao, Yuan, Yinyin, Adams, Sylvia, Bartlett, John Mark Seaverns, Loibl, Sibylle, Denkert, Carsten, Savas, Peter, Loi, Sherene, Salgado, Roberto, Specht Stovgaard, Elisabeth, Akturk, Guray, Bouchmaa, Najat, Pathologie, Cancer, Page, David B, Broeckx, Glenn, Jahangir, Chowdhury Arif, Verbandt, Sara, Gupta, Rajarsi R, Thagaard, Jeppe, Khiroya, Reena, Kos, Zuzana, Abduljabbar, Khalid, Acosta Haab, Gabriela, Acs, Balazs, Almeida, Jonas S, Alvarado-Cabrero, Isabel, Azmoudeh-Ardalan, Farid, Badve, Sunil, Baharun, Nurkhairul Bariyah, Bellolio, Enrique R, Bheemaraju, Vydehi, Blenman, Kim Rm, Botinelly Mendonça Fujimoto, Luciana, Burgues, Octavio, Cheang, Maggie Chon U, Ciompi, Francesco, Cooper, Lee Ad, Coosemans, An, Corredor, Germán, Dantas Portela, Flavio Luis, Deman, Frederik, Demaria, Sandra, Dudgeon, Sarah N, Elghazawy, Mahmoud, Ely, Scott, Fernandez-Martín, Claudio, Fineberg, Susan, Fox, Stephen B, Gallagher, William M, Giltnane, Jennifer M, Gnjatic, Sacha, Gonzalez-Ericsson, Paula I, Grigoriadis, Anita, Halama, Niels, Hanna, Matthew G, Harbhajanka, Aparna, Hardas, Alexandros, Hart, Steven N, Hartman, Johan, Hewitt, Stephen, Hida, Akira I, Horlings, Hugo M, Husain, Zaheed, Hytopoulos, Evangelos, Irshad, Sheeba, Janssen, Emiel Am, Kahila, Mohamed, Kataoka, Tatsuki R, Kawaguchi, Kosuke, Kharidehal, Durga, Khramtsov, Andrey I, Kiraz, Umay, Kirtani, Pawan, Kodach, Liudmila L, Korski, Konstanty, Kovács, Anikó, Laenkholm, Anne-Vibeke, Lang-Schwarz, Corinna, Larsimont, Denis, Lennerz, Jochen K, Lerousseau, Marvin, Li, Xiaoxian, Ly, Amy, Madabhushi, Anant, Maley, Sai K, Manur Narasimhamurthy, Vidya, Marks, Douglas K, McDonald, Elizabeth S, Mehrotra, Ravi, Michiels, Stefan, Minhas, Fayyaz Ul Amir Afsar, Mittal, Shachi, Moore, David A, Mushtaq, Shamim, Nighat, Hussain, Papathomas, Thomas, Penault-Llorca, Frederique, Perera, Rashindrie D, Pinard, Christopher J, Pinto-Cardenas, Juan Carlos, Pruneri, Giancarlo, Pusztai, Lajos, Rahman, Arman, Rajpoot, Nasir Mahmood, Rapoport, Bernardo Leon, Rau, Tilman T, Reis-Filho, Jorge S, Ribeiro, Joana M, Rimm, David, Salomon, Anne-Vincent, Salto-Tellez, Manuel, Saltz, Joel, Sayed, Shahin, Siziopikou, Kalliopi P, Sotiriou, Christos, Stenzinger, Albrecht, Sughayer, Maher A, Sur, Daniel, Symmans, Fraser, Tanaka, Sunao, Taxter, Timothy, Tejpar, Sabine, Teuwen, Jonas, Thompson, E Aubrey, Tramm, Trine, Tran, William T, van der Laak, Jeroen, van Diest, Paul J, Verghese, Gregory E, Viale, Giuseppe, Vieth, Michael, Wahab, Noorul, Walter, Thomas, Waumans, Yannick, Wen, Hannah Y, Yang, Wentao, Yuan, Yinyin, Adams, Sylvia, Bartlett, John Mark Seaverns, Loibl, Sibylle, Denkert, Carsten, Savas, Peter, Loi, Sherene, Salgado, Roberto, Specht Stovgaard, Elisabeth, Akturk, Guray, and Bouchmaa, Najat

Published
2023

21. Pitfalls in machine learning-based assessment of tumor-infiltrating lymphocytes in breast cancer:a report of the international immuno-oncology biomarker working group

Author

Thagaard, Jeppe, Broeckx, Glenn, Page, David B., Jahangir, Chowdhury Arif, Verbandt, Sara, Kos, Zuzana, Gupta, Rajarsi, Khiroya, Reena, Abduljabbar, Khalid, Acosta Haab, Gabriela, Acs, Balazs, Akturk, Guray, Almeida, Jonas S., Alvarado-Cabrero, Isabel, Amgad, Mohamed, Azmoudeh-Ardalan, Farid, Badve, Sunil, Baharun, Nurkhairul Bariyah, Balslev, Eva, Bellolio, Enrique R., Bheemaraju, Vydehi, Blenman, Kim R.M., Botinelly Mendonça Fujimoto, Luciana, Bouchmaa, Najat, Burgues, Octavio, Chardas, Alexandros, Chon U Cheang, Maggie, Ciompi, Francesco, Cooper, Lee A.D., Coosemans, An, Corredor, Germán, Dahl, Anders B., Dantas Portela, Flavio Luis, Deman, Frederik, Demaria, Sandra, Doré Hansen, Johan, Dudgeon, Sarah N., Ebstrup, Thomas, Elghazawy, Mahmoud, Fernandez-Martín, Claudio, Fox, Stephen B., Gallagher, William M., Giltnane, Jennifer M., Gnjatic, Sacha, Gonzalez-Ericsson, Paula I., Grigoriadis, Anita, Halama, Niels, Hanna, Matthew G., Harbhajanka, Aparna, Hart, Steven N., Hartman, Johan, Hauberg, Søren, Hewitt, Stephen, Hida, Akira I., Horlings, Hugo M., Husain, Zaheed, Hytopoulos, Evangelos, Irshad, Sheeba, Janssen, Emiel A.M., Kahila, Mohamed, Kataoka, Tatsuki R., Kawaguchi, Kosuke, Kharidehal, Durga, Khramtsov, Andrey I., Kiraz, Umay, Kirtani, Pawan, Kodach, Liudmila L., Korski, Konstanty, Kovács, Anikó, Laenkholm, Anne Vibeke, Lang-Schwarz, Corinna, Larsimont, Denis, Lennerz, Jochen K., Lerousseau, Marvin, Li, Xiaoxian, Ly, Amy, Madabhushi, Anant, Maley, Sai K., Manur Narasimhamurthy, Vidya, Marks, Douglas K., McDonald, Elizabeth S., Mehrotra, Ravi, Michiels, Stefan, Minhas, Fayyaz ul Amir Afsar, Mittal, Shachi, Moore, David A., Mushtaq, Shamim, Nighat, Hussain, Papathomas, Thomas, Penault-Llorca, Frederique, Perera, Rashindrie D., Pinard, Christopher J., Pinto-Cardenas, Juan Carlos, Pruneri, Giancarlo, Pusztai, Lajos, Rahman, Arman, Rajpoot, Nasir Mahmood, Rapoport, Bernardo Leon, Rau, Tilman T., Reis-Filho, Jorge S., Ribeiro, Joana M., Rimm, David, Roslind, Anne, Vincent-Salomon, Anne, Salto-Tellez, Manuel, Saltz, Joel, Sayed, Shahin, Scott, Ely, Siziopikou, Kalliopi P., Sotiriou, Christos, Stenzinger, Albrecht, Sughayer, Maher A., Sur, Daniel, Fineberg, Susan, Symmans, Fraser, Tanaka, Sunao, Taxter, Timothy, Tejpar, Sabine, Teuwen, Jonas, Thompson, E. Aubrey, Tramm, Trine, Tran, William T., van der Laak, Jeroen, van Diest, Paul J., Verghese, Gregory E., Viale, Giuseppe, Vieth, Michael, Wahab, Noorul, Walter, Thomas, Waumans, Yannick, Wen, Hannah Y., Yang, Wentao, Yuan, Yinyin, Zin, Reena Md, Adams, Sylvia, Bartlett, John, Loibl, Sibylle, Denkert, Carsten, Savas, Peter, Loi, Sherene, Salgado, Roberto, Specht Stovgaard, Elisabeth, Thagaard, Jeppe, Broeckx, Glenn, Page, David B., Jahangir, Chowdhury Arif, Verbandt, Sara, Kos, Zuzana, Gupta, Rajarsi, Khiroya, Reena, Abduljabbar, Khalid, Acosta Haab, Gabriela, Acs, Balazs, Akturk, Guray, Almeida, Jonas S., Alvarado-Cabrero, Isabel, Amgad, Mohamed, Azmoudeh-Ardalan, Farid, Badve, Sunil, Baharun, Nurkhairul Bariyah, Balslev, Eva, Bellolio, Enrique R., Bheemaraju, Vydehi, Blenman, Kim R.M., Botinelly Mendonça Fujimoto, Luciana, Bouchmaa, Najat, Burgues, Octavio, Chardas, Alexandros, Chon U Cheang, Maggie, Ciompi, Francesco, Cooper, Lee A.D., Coosemans, An, Corredor, Germán, Dahl, Anders B., Dantas Portela, Flavio Luis, Deman, Frederik, Demaria, Sandra, Doré Hansen, Johan, Dudgeon, Sarah N., Ebstrup, Thomas, Elghazawy, Mahmoud, Fernandez-Martín, Claudio, Fox, Stephen B., Gallagher, William M., Giltnane, Jennifer M., Gnjatic, Sacha, Gonzalez-Ericsson, Paula I., Grigoriadis, Anita, Halama, Niels, Hanna, Matthew G., Harbhajanka, Aparna, Hart, Steven N., Hartman, Johan, Hauberg, Søren, Hewitt, Stephen, Hida, Akira I., Horlings, Hugo M., Husain, Zaheed, Hytopoulos, Evangelos, Irshad, Sheeba, Janssen, Emiel A.M., Kahila, Mohamed, Kataoka, Tatsuki R., Kawaguchi, Kosuke, Kharidehal, Durga, Khramtsov, Andrey I., Kiraz, Umay, Kirtani, Pawan, Kodach, Liudmila L., Korski, Konstanty, Kovács, Anikó, Laenkholm, Anne Vibeke, Lang-Schwarz, Corinna, Larsimont, Denis, Lennerz, Jochen K., Lerousseau, Marvin, Li, Xiaoxian, Ly, Amy, Madabhushi, Anant, Maley, Sai K., Manur Narasimhamurthy, Vidya, Marks, Douglas K., McDonald, Elizabeth S., Mehrotra, Ravi, Michiels, Stefan, Minhas, Fayyaz ul Amir Afsar, Mittal, Shachi, Moore, David A., Mushtaq, Shamim, Nighat, Hussain, Papathomas, Thomas, Penault-Llorca, Frederique, Perera, Rashindrie D., Pinard, Christopher J., Pinto-Cardenas, Juan Carlos, Pruneri, Giancarlo, Pusztai, Lajos, Rahman, Arman, Rajpoot, Nasir Mahmood, Rapoport, Bernardo Leon, Rau, Tilman T., Reis-Filho, Jorge S., Ribeiro, Joana M., Rimm, David, Roslind, Anne, Vincent-Salomon, Anne, Salto-Tellez, Manuel, Saltz, Joel, Sayed, Shahin, Scott, Ely, Siziopikou, Kalliopi P., Sotiriou, Christos, Stenzinger, Albrecht, Sughayer, Maher A., Sur, Daniel, Fineberg, Susan, Symmans, Fraser, Tanaka, Sunao, Taxter, Timothy, Tejpar, Sabine, Teuwen, Jonas, Thompson, E. Aubrey, Tramm, Trine, Tran, William T., van der Laak, Jeroen, van Diest, Paul J., Verghese, Gregory E., Viale, Giuseppe, Vieth, Michael, Wahab, Noorul, Walter, Thomas, Waumans, Yannick, Wen, Hannah Y., Yang, Wentao, Yuan, Yinyin, Zin, Reena Md, Adams, Sylvia, Bartlett, John, Loibl, Sibylle, Denkert, Carsten, Savas, Peter, Loi, Sherene, Salgado, Roberto, and Specht Stovgaard, Elisabeth

Abstract

The clinical significance of the tumor-immune interaction in breast cancer is now established, and tumor-infiltrating lymphocytes (TILs) have emerged as predictive and prognostic biomarkers for patients with triple-negative (estrogen receptor, progesterone receptor, and HER2-negative) breast cancer and HER2-positive breast cancer. How computational assessments of TILs might complement manual TIL assessment in trial and daily practices is currently debated. Recent efforts to use machine learning (ML) to automatically evaluate TILs have shown promising results. We review state-of-the-art approaches and identify pitfalls and challenges of automated TIL evaluation by studying the root cause of ML discordances in comparison to manual TIL quantification. We categorize our findings into four main topics: (1) technical slide issues, (2) ML and image analysis aspects, (3) data challenges, and (4) validation issues. The main reason for discordant assessments is the inclusion of false-positive areas or cells identified by performance on certain tissue patterns or design choices in the computational implementation. To aid the adoption of ML for TIL assessment, we provide an in-depth discussion of ML and image analysis, including validation issues that need to be considered before reliable computational reporting of TILs can be incorporated into the trial and routine clinical management of patients with triple-negative breast cancer.

Published
2023

22. Single cell dynamics of tumor specificity vs bystander activity in CD8+ T cells define the diverse immune landscapes in colorectal cancer.

Author

Borràs, Daniel Morales, Verbandt, Sara, Ausserhofer, Markus, Sturm, Gregor, Lim, Jinyeong, Verge, Gil Arasa, Vanmeerbeek, Isaure, Laureano, Raquel S., Govaerts, Jannes, Sprooten, Jenny, Hong, Yourae, Wall, Rebecca, De Hertogh, Gert, Sagaert, Xavier, Bislenghi, Gabriele, D'Hoore, André, Wolthuis, Albert, Finotello, Francesca, Park, Woong-Yang, and Naulaerts, Stefan

Subjects
GUT microbiome, T cells, T cell receptors, COLORECTAL cancer, TUMOR classification, IMMUNE checkpoint proteins
Abstract

CD8+ T cell activation via immune checkpoint blockade (ICB) is successful in microsatellite instable (MSI) colorectal cancer (CRC) patients. By comparison, the success of immunotherapy against microsatellite stable (MSS) CRC is limited. Little is known about the most critical features of CRC CD8+ T cells that together determine the diverse immune landscapes and contrasting ICB responses. Hence, we pursued a deep single cell mapping of CRC CD8+ T cells on transcriptomic and T cell receptor (TCR) repertoire levels in a diverse patient cohort, with additional surface proteome validation. This revealed that CRC CD8+ T cell dynamics are underscored by complex interactions between interferon-γ signaling, tumor reactivity, TCR repertoire, (predicted) TCR antigen-specificities, and environmental cues like gut microbiome or colon tissue-specific 'self-like' features. MSI CRC CD8+ T cells showed tumor-specific activation reminiscent of canonical 'T cell hot' tumors, whereas the MSS CRC CD8+ T cells exhibited tumor unspecific or bystander-like features. This was accompanied by inflammation reminiscent of 'pseudo-T cell hot' tumors. Consequently, MSI and MSS CRC CD8+ T cells showed overlapping phenotypic features that differed dramatically in their TCR antigen-specificities. Given their high discriminating potential for CD8+ T cell features/specificities, we used the single cell tumor-reactive signaling modules in CD8+ T cells to build a bulk tumor transcriptome classification for CRC patients. This "Immune Subtype Classification" (ISC) successfully distinguished various tumoral immune landscapes that showed prognostic value and predicted immunotherapy responses in CRC patients. Thus, we deliver a unique map of CRC CD8+ T cells that drives a novel tumor immune landscape classification, with relevance for immunotherapy decision-making. [ABSTRACT FROM AUTHOR]

Published
2023
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23. A Pan-cancer Blueprint of the Heterogeneous Tumour Microenvironment Revealed by Single-Cell Profiling

Author

Qian, Junbin, primary, Olbrecht, Siel, additional, Boeckx, Bram, additional, Vos, Hanne, additional, Laoui, Damya, additional, Etlioglu, Emre, additional, Wauters, Els, additional, Pomella, Valentina, additional, Verbandt, Sara, additional, Busschaert, Pieter, additional, Bassez, Ayse, additional, Franken, Amelie, additional, Bempt, Marlies Vanden, additional, Xiong, Jieyi, additional, Weynand, Birgit, additional, van Herck, Yannick, additional, Antoranz, Asier, additional, Bosisio, Francesca Maria, additional, Thienpont, Bernard, additional, Floris, Giuseppe, additional, Vergote, Ignace, additional, Smeets, Ann, additional, Tejpar, Sabine, additional, and Lambrechts, Diether, additional

Published
2020
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24. Transition between fermentation and respiration determines history-dependent behavior in fluctuating carbon sources

Author

Cerulus, Bram, primary, Jariani, Abbas, additional, Perez-Samper, Gemma, additional, Vermeersch, Lieselotte, additional, Pietsch, Julian MJ, additional, Crane, Matthew M, additional, New, Aaron M, additional, Gallone, Brigida, additional, Roncoroni, Miguel, additional, Dzialo, Maria C, additional, Govers, Sander K, additional, Hendrickx, Jhana O, additional, Galle, Eva, additional, Coomans, Maarten, additional, Berden, Pieter, additional, Verbandt, Sara, additional, Swain, Peter S, additional, and Verstrepen, Kevin J, additional

Published
2018
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25. Author response: Transition between fermentation and respiration determines history-dependent behavior in fluctuating carbon sources

Author

Cerulus, Bram, primary, Jariani, Abbas, additional, Perez-Samper, Gemma, additional, Vermeersch, Lieselotte, additional, Pietsch, Julian MJ, additional, Crane, Matthew M, additional, New, Aaron M, additional, Gallone, Brigida, additional, Roncoroni, Miguel, additional, Dzialo, Maria C, additional, Govers, Sander K, additional, Hendrickx, Jhana O, additional, Galle, Eva, additional, Coomans, Maarten, additional, Berden, Pieter, additional, Verbandt, Sara, additional, Swain, Peter S, additional, and Verstrepen, Kevin J, additional

Published
2018
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26. Identification of survival-promoting OSIP108 peptide variants and their internalization in human cells

Author

Verbandt, Sara, Troeira Henriques, Sonia, Spincemaille, Pieter, Harvey, Peta, Chandhok, Gursimran, Sauer, Vanessa, De Coninck, Barbara, Cassiman, David, Craik, David, Cammue, Bruno, De Cremer, Kaat, Thevissen, Karin, Verbandt, Sara, Troeira Henriques, Sonia, Spincemaille, Pieter, Harvey, Peta, Chandhok, Gursimran, Sauer, Vanessa, De Coninck, Barbara, Cassiman, David, Craik, David, Cammue, Bruno, De Cremer, Kaat, and Thevissen, Karin

Abstract

he plant-derived decapeptide OSIP108 increases tolerance of yeast and human cells to apoptosis-inducing agents, such as copper and cisplatin. We performed a whole amino acid scan of OSIP108 and conducted structure-activity relationship studies on the induction of cisplatin tolerance (CT) in yeast. The use of cisplatin as apoptosis-inducing trigger in this study should be considered as a tool to better understand the survival-promoting nature of OSIP108 and not for purposes related to anti-cancer treatment. We found that charged residues (Arg, His, Lys, Glu or Asp) or a Pro on positions 4-7 improved OSIP108 activity by 10% or more. The variant OSIP108[G7P] induced the most pronounced tolerance to toxic concentrations of copper and cisplatin in yeast and/or HepG2 cells. Both OSIP108 and OSIP108[G7P] were shown to internalize equally into HeLa cells, but at a higher rate than the inactive OSIP108[E10A], suggesting that the peptides can internalize into cells and that OSIP108 activity is dependent on subsequent intracellular interactions. In conclusion, our studies demonstrated that tolerance/survival-promoting properties of OSIP108 can be significantly improved by single amino acid substitutions, and that these properties are dependent on (an) intracellular target(s), yet to be determined.

Published
2017

27. The Antifungal Plant Defensin HsAFP1 Is a Phosphatidic Acid-Interacting Peptide Inducing Membrane Permeabilization

Author

Cools, Tanne L., primary, Vriens, Kim, additional, Struyfs, Caroline, additional, Verbandt, Sara, additional, Ramada, Marcelo H. S., additional, Brand, Guilherme D., additional, Bloch, Carlos, additional, Koch, Barbara, additional, Traven, Ana, additional, Drijfhout, Jan W., additional, Demuyser, Liesbeth, additional, Kucharíková, Soňa, additional, Van Dijck, Patrick, additional, Spasic, Dragana, additional, Lammertyn, Jeroen, additional, Cammue, Bruno P. A., additional, and Thevissen, Karin, additional

Published
2017
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28. Identification of survival-promoting OSIP108 peptide variants and their internalization in human cells

Author

Verbandt, Sara, primary, Henriques, Sónia Troeira, additional, Spincemaille, Pieter, additional, Harvey, Peta J., additional, Chandhok, Gursimran, additional, Sauer, Vanessa, additional, De Coninck, Barbara, additional, Cassiman, David, additional, Craik, David J., additional, Cammue, Bruno P.A., additional, De Cremer, Kaat, additional, and Thevissen, Karin, additional

Published
2017
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30. IL-1R signaling drives enteric glia-macrophage interactions in colorectal cancer.

Author

van Baarle L, De Simone V, Schneider L, Santhosh S, Abdurahiman S, Biscu F, Schneider R, Zanoletti L, Siqueira de Mello R, Verbandt S, Hu Z, Stakenborg M, Ke BJ, Stakenborg N, Salvador Laureano R, García-Reyes B, Henn J, Toma M, Vanmechelen M, Boeckxstaens G, De Smet F, Garg AD, Ibiza S, Tejpar S, Wehner S, and Matteoli G

Subjects
Animals, Humans, Mice, Macrophages metabolism, Macrophages immunology, Receptors, Interleukin-1 metabolism, Receptors, Interleukin-1 genetics, Tumor-Associated Macrophages immunology, Tumor-Associated Macrophages metabolism, Interleukin-6 metabolism, Monocytes metabolism, Monocytes immunology, Mice, Inbred C57BL, Cell Communication, Cell Differentiation, Cell Line, Tumor, Female, Colorectal Neoplasms pathology, Colorectal Neoplasms immunology, Colorectal Neoplasms metabolism, Colorectal Neoplasms genetics, Tumor Microenvironment immunology, Neuroglia metabolism, Signal Transduction
Abstract

Enteric glia have been recently recognized as key components of the colonic tumor microenvironment indicating their potential role in colorectal cancer pathogenesis. Although enteric glia modulate immune responses in other intestinal diseases, their interaction with the colorectal cancer immune cell compartment remains unclear. Through a combination of single-cell and bulk RNA-sequencing, both in murine models and patients, here we find that enteric glia acquire an immunomodulatory phenotype by bi-directional communication with tumor-infiltrating monocytes. The latter direct a reactive enteric glial cell phenotypic and functional switch via glial IL-1R signaling. In turn, tumor glia promote monocyte differentiation towards pro-tumorigenic SPP1 + tumor-associated macrophages by IL-6 release. Enteric glia cell abundancy correlates with worse disease outcomes in preclinical models and colorectal cancer patients. Thereby, our study reveals a neuroimmune interaction between enteric glia and tumor-associated macrophages in the colorectal tumor microenvironment, providing insights into colorectal cancer pathogenesis., (© 2024. The Author(s).)

Published
2024
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31. Neoantigen identification: Technological advances and challenges.

Author

Pu T, Peddle A, Zhu J, Tejpar S, and Verbandt S

Subjects
Humans, Immunotherapy, Antigens, Neoplasm genetics, Neoplasms genetics, Neoplasms therapy
Abstract

Neoantigens have emerged as promising targets for cutting-edge immunotherapies, such as cancer vaccines and adoptive cell therapy. These neoantigens are unique to tumors and arise exclusively from somatic mutations or non-genomic aberrations in tumor proteins. They encompass a wide range of alterations, including genomic mutations, post-transcriptomic variants, and viral oncoproteins. With the advancements in technology, the identification of immunogenic neoantigens has seen rapid progress, raising new opportunities for enhancing their clinical significance. Prediction of neoantigens necessitates the acquisition of high-quality samples and sequencing data, followed by mutation calling. Subsequently, the pipeline involves integrating various tools that can predict the expression, processing, binding, and recognition potential of neoantigens. However, the continuous improvement of computational tools is constrained by the availability of datasets which contain validated immunogenic neoantigens. This review article aims to provide a comprehensive summary of the current knowledge as well as limitations in neoantigen prediction and validation. Additionally, it delves into the origin and biological role of neoantigens, offering a deeper understanding of their significance in the field of cancer immunotherapy. This article thus seeks to contribute to the ongoing efforts to harness neoantigens as powerful weapons in the fight against cancer., Competing Interests: Conflicts of interest The authors declare that there is no conflict of interest regarding the publication of this paper., (Copyright © 2024 Elsevier Inc. All rights are reserved, including those for text and data mining, AI training, and similar technologies.)

Published
2024
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